When you say “the running register total", is that the Cash Bal column in the account's Transaction List (register)? And when the totlal is “out of wack”, does the cash balance not change when you enter a transaction like Bought, Sold, or Div that should change it? And is a Cash Balance Adustment automatically entered for each of these transactons, preventing the cash balance from changing?
If so, that certainly sounds like you have a Placeholder for that security at a later date than the date of the transaction you are entering. Please check the setting at Edit > Preferences > Investments to make sure the “Show hidden transactions” box is checked, and make sure there are no Placeholders.